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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaatgatagtaacctccacgtaacagcaatacctcaactaattgagcagttacttatgtctgtttcgaatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG

Basic information

species Zea mays
transcript GRMZM5G846339_T01
intron # 3
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|76017486|gb|DT944656.1|DT944656
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148945518|gb|EC890763.2|EC890763
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149004827|gb|EE039332.2|EE039332
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|76915578|gb|DV166043.1|DV166043
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149112888|gb|EE295684.2|EE295684
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211013669|gb|FL365579.1|FL365579
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211367815|gb|FL346930.1|FL346930
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211288821|gb|FL321201.1|FL321201
EST:     GCTTCCTTCSTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211535602|gb|FL367699.1|FL367699
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149070557|gb|EE158959.2|EE158959
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148950258|gb|EC895810.2|EC895810
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148965790|gb|EE016673.2|EE016673
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagcaatacctcaactaattgagcagttacttatgtctgtttcgaatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG
             aactaat  putative branch site (score: 202)
             aactaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaatgatagtaacctccacgtaacagcaatacctcaactaattgagcagttacttatgtctgtttcgaatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT